FOXN2

forkhead box N2, the group of Forkhead boxes

Basic information

Region (hg38): 2:48314636-48379295

Previous symbols: [ "HTLF" ]

Links

ENSG00000170802 ∙ NCBI:3344 ∙ OMIM:143089 ∙ HGNC:5281 ∙ Uniprot:P32314 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FOXN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOXN2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	2

Variants in FOXN2

This is a list of pathogenic ClinVar variants found in the FOXN2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-48346242-G-C		not specified	Uncertain significance (Nov 07, 2023)
2-48346275-A-T		not specified	Uncertain significance (Sep 16, 2021)
2-48346279-C-T		not specified	Uncertain significance (Mar 15, 2024)
2-48346339-C-G		not specified	Uncertain significance (Sep 01, 2021)
2-48346455-A-G		not specified	Uncertain significance (Sep 25, 2023)
2-48346461-A-C		not specified	Uncertain significance (Apr 05, 2023)
2-48346468-T-G		not specified	Uncertain significance (Aug 17, 2022)
2-48346573-T-C		not specified	Uncertain significance (Aug 10, 2023)
2-48346602-A-G		not specified	Uncertain significance (Jan 16, 2024)
2-48346736-A-G			Benign (May 17, 2018)
2-48359051-A-C		not specified	Uncertain significance (Feb 28, 2024)
2-48359081-C-T		not specified	Uncertain significance (Nov 09, 2021)
2-48359096-A-G		not specified	Uncertain significance (Oct 27, 2021)
2-48362690-A-G		not specified	Uncertain significance (Feb 17, 2024)
2-48362696-G-A		not specified	Likely benign (Apr 11, 2023)
2-48373320-G-C		not specified	Uncertain significance (Dec 08, 2023)
2-48373323-G-A		not specified	Uncertain significance (Aug 09, 2021)
2-48373336-T-A		not specified	Uncertain significance (Feb 15, 2023)
2-48374946-G-A		not specified	Uncertain significance (Jul 30, 2023)
2-48374950-T-C		not specified	Uncertain significance (Mar 01, 2023)
2-48374983-A-G		not specified	Uncertain significance (Aug 15, 2023)
2-48375004-T-C		not specified	Uncertain significance (Aug 17, 2022)
2-48375037-A-G		not specified	Uncertain significance (Jun 07, 2023)
2-48375092-A-T			Benign (Dec 31, 2019)
2-48375114-C-G		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOXN2	protein_coding	protein_coding	ENST00000340553	5	64658

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.497	0.503	125732	0	11	125743	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.587	254	229	1.11	0.0000112	2835
Missense in Polyphen		63	72.537	0.86852		931
Synonymous	-0.633	89	81.7	1.09	0.00000416	819
Loss of Function	3.21	4	19.2	0.209	0.00000114	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000621	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000546	0.0000544
South Asian	0.000174	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to the purine-rich region in HTLV-I LTR.

Recessive Scores

• pRec: 0.165

Intolerance Scores

• loftool: 0.123
• rvis_EVS: -0.74
• rvis_percentile_EVS: 13.94

Haploinsufficiency Scores

• pHI: 0.612
• hipred: Y
• hipred_score: 0.518
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Foxn2

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;skeletal muscle cell differentiation
• Cellular component: nucleus;intracellular membrane-bounded organelle
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding